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The Allen Human Brain Atlas offers three types of searches to allow a user to: (1) obtain gene expression data for specific genes (or probes) of interest (Gene Search); (2) compare expression between different anatomic regions (Differential Search); and (3) use a 'seed' gene to find other genes with similar expression patterns (Find Correlates).

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GENE SEARCH

To search for probes associated with a specific gene or group of genes, select the Gene Search radio button and type the gene name, gene symbol, Entrez Gene ID or probe ID in the search box (multiple genes searches require an OR between gene names) before clicking the "Search" button. To show exact matches to your search query click the "Show exact matches only" box.


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Boolean Syntax

The following special operators can be used to build queries:

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To download your search results, click the "Download this data" link at the bottom left of the heatmap.

Differential Search

To find genes that show enrichment of expression in one region compared to another region, use the Differential Search mode. Select the "Differential Search" radio button. To find genes or probes with an enhanced gene expression profile in one or more brain regions when compared to one or more other brain regions by entering the target structure(s) in the top search box (separate structures with a semicolon) and your contrast structure(s) in the bottom search box and click the Search button.

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The search returns will show genes exhibiting higher expression in the target region(s) compared to the contrast region(s).Search results are sorted either by p-value or fold change, indicated by the arrow on the buttons over the column of genes. To alter the sort parameter, click on either the "p-value" or the "fold change" button.

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To filter your results by structure or by donor, click on the "Filter Heatmap" button below the heatmap.

To perform the previous search in reverse, click the toggle button to the left of the Search button. To download your search results, click the "Download this data" link at the bottom left of the heatmap.

Mouse Differential Search

The "Mouse Differential Search" function enables side by side viewing and comparison of differential search across the human microarray and the mouse ISH datasets. Select the "Mouse Differential Search" radio button. To find genes with higher expression in one structure compared to another structure, select a target brain structure in the top drop-down box and a contrast region in the bottom drop-down box and click on the Search button.

Search results

The return list is generated by first executing a differential search query in the human microarray dataset. Experiments for each gene are grouped together and ordered by maximum fold-change. For each gene in the human microarray return list, associated experiments in the mouse ISH dataset are identified; fold-change values are computed and displayed. Note that NCBI HomoloGene data is used to link genes across organisms. Click on the dataset column heading to toggle the primary dataset selection.

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For human brain data, microarray data is visualized as a heatmap where each column represents a tissue sample in ontological order. Heatmap color represents the z-score over a probe ranging from green (z-score of -3 and below) through black to red (z-score of +3 and above). Hover over any position in the heatmap to obtain the associated tissue sample structural annotation.

Gene Classification

When you are viewing heatmap data, there will be a "Gene Classification" radio button available. When the gene classification radio button is selected, you can search for enhanced gene expression from one of the categories in the drop down menu.

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To download your search results, click the "Download this data" link at the bottom left of the heatmap.

Correlative Search

In using gene expression databases, a "search by example" feature is also highly desirable as genes with similar expression patterns may be related in function. The Find Correlates search utility will accomplish this function. This search by example facility is also available in the Allen Mouse Brain Atlas, Allen Developing Mouse Brain Atlas and the BrainSpan atlas of the developing human brain.

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Once you have identified a gene of interest, to find other genes with spatial expression profiles similar to your gene of interest, first select your probe by clicking on any cell in the heat map related to that probe. You will see that probe listed in the box above the right hand side of the heat map. Then select the brain structure(s) in which you would like to see a similar expression pattern, and click "Find Correlates". This action will return probes with a similar expression profile to brain region(s) in which you are interested.

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You can see "anti-correlated" returns by toggling the sort order on column "r" or scrolling to the bottom of the heatmap.

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To download your search results, click the "Download this data" link at the bottom left of the heatmap.

Download Search Results

To download your search results, click the "Download this data" link at the bottom left of the heatmap. You will have the option of downloading up to 2000 genes at a time starting from any position in the heatmap. Your start position can be determined from the counter in the top left corner of the heatmap (see screenshot).

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In the top right hand corner of the heat map is a toggle button, which when clicked will sort the heat map data either by donor or by structure.

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Data Aggregation and Normalization

Unless viewing data on the lowest possible resolution, the heat maps presented on this site are based on data aggregated within brain structures. That is, when there are multiple samples for a given structure, the value represented in the heat map will be the average of those sample values.

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For each probe, we have provided an anatomical abstract view of the gene expression pattern of each donor. Regions of the brain are listed in each of the views, and the text can be removed by clicking on the 'Labels' button. The cortical gene expression patterns (3) are displayed on an inflated cortical surface (outer and inner surfaces of the left hemisphere). Subcortical structures of the brain are represented from a frontal view (4), and subcortical as well as brainstem structures are shown in a side view (5). Hovering your mouse over an annotated structure will bring up the structure name as well as the normalized and raw expression level values. Clicking on a structure will bring up links to the #Multiplanar Viewer and the Brain Explorer.

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Multiplanar Viewer

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